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Kodgire P, Dixit M, Rao KK. ScoC and SinR negatively regulate epr by corepression in Bacillus subtilis. J Bacteriol 2006; 188:6425-8. [PMID: 16923912 PMCID: PMC1595376 DOI: 10.1128/jb.00427-06] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Negative regulation of epr in Bacillus subtilis 168 is mediated jointly by both ScoC and SinR, which bind to their respective target sites 62 bp apart. Increasing the distance between the two sites abolishes repression, indicating that the two proteins interact, thereby suggesting a mechanism of corepression.
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Affiliation(s)
- Prashant Kodgire
- School of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
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2
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Pedersen M, Kilstrup M, Hammer K. Identification of DNA-binding sites for the activator involved in late transcription of the temperate lactococcal phage TP901-1. Virology 2006; 345:446-56. [PMID: 16297953 DOI: 10.1016/j.virol.2005.10.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2005] [Revised: 09/27/2005] [Accepted: 10/08/2005] [Indexed: 11/22/2022]
Abstract
Alt, encoded by the lactococcal phage TP901-1, is needed for late transcription. We identify Alt as a DNA-binding protein, and footprint analysis shows that Alt binds to a region containing four imperfect direct repeats (ALT boxes) located -76 to -32 relative to the P(late) transcriptional start site. The importance of the ALT boxes was confirmed by deletion of one or two ALT boxes and by introducing mutations in ALT boxes 1 and 4. Alt is proposed to act as a tetramer or higher multimer activating transcription of TP901-1 late genes by binding to the four ALT boxes, and bending of the DNA may be important for transcriptional activation of P(late). Furthermore, our results suggest that DNA replication may be required for late transcription in TP901-1. Additionally, we identify gp28 of the related lactococcal phage Tuc2009 as an activator and show that the activators required for late transcription in TP901-1 and Tuc2009 are interchangeable.
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Affiliation(s)
- Margit Pedersen
- Department of Microbial Physiology and Genetics, BioCentrum-DTU, Technical University of Denmark, DK-2800 Lyngby, Denmark
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3
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Łobocka MB, Rose DJ, Plunkett G, Rusin M, Samojedny A, Lehnherr H, Yarmolinsky MB, Blattner FR. Genome of bacteriophage P1. J Bacteriol 2004; 186:7032-68. [PMID: 15489417 PMCID: PMC523184 DOI: 10.1128/jb.186.21.7032-7068.2004] [Citation(s) in RCA: 193] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2004] [Accepted: 07/09/2004] [Indexed: 11/20/2022] Open
Abstract
P1 is a bacteriophage of Escherichia coli and other enteric bacteria. It lysogenizes its hosts as a circular, low-copy-number plasmid. We have determined the complete nucleotide sequences of two strains of a P1 thermoinducible mutant, P1 c1-100. The P1 genome (93,601 bp) contains at least 117 genes, of which almost two-thirds had not been sequenced previously and 49 have no homologs in other organisms. Protein-coding genes occupy 92% of the genome and are organized in 45 operons, of which four are decisive for the choice between lysis and lysogeny. Four others ensure plasmid maintenance. The majority of the remaining 37 operons are involved in lytic development. Seventeen operons are transcribed from sigma(70) promoters directly controlled by the master phage repressor C1. Late operons are transcribed from promoters recognized by the E. coli RNA polymerase holoenzyme in the presence of the Lpa protein, the product of a C1-controlled P1 gene. Three species of P1-encoded tRNAs provide differential controls of translation, and a P1-encoded DNA methyltransferase with putative bifunctionality influences transcription, replication, and DNA packaging. The genome is particularly rich in Chi recombinogenic sites. The base content and distribution in P1 DNA indicate that replication of P1 from its plasmid origin had more impact on the base compositional asymmetries of the P1 genome than replication from the lytic origin of replication.
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Affiliation(s)
- Małgorzata B Łobocka
- Department of Microbial Biochemistry, Institute of Biochemistry and Biophysics of the Polish Academy of Sciences, Ul. Pawinskiego 5A, 02-106 Warsaw, Poland.
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4
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Abstract
Bacterial plasmids of low copy number, P1 prophage among them, are actively partitioned to nascent daughter cells. The process is typically mediated by a pair of plasmid-encoded proteins and a cis-acting DNA site or cluster of sites, referred to as the plasmid centromere. P1 ParB protein, which binds to the P1 centromere (parS), can spread for several kilobases along flanking DNA. We argue that studies of mutant ParB that demonstrated a strong correlation between spreading capacity and the ability to engage in partitioning may be misleading, and describe here a critical test of the dependence of partitioning on the spreading of the wild-type protein. Physical constraints imposed on the spreading of P1 ParB were found to have only a minor, but reproducible, effect on partitioning. We conclude that, whereas extensive ParB spreading is not required for partitioning, spreading may have an auxiliary role in the process.
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Affiliation(s)
- Oleg Rodionov
- Laboratory of Biochemistry, National Cancer Institute, NIH, Bldg 37, Room 6044C, 37 Convent Drive, Bethesda, MD 20892-4255, USA
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5
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Hansen AM, Lehnherr H, Wang X, Mobley V, Jin DJ. Escherichia coli SspA is a transcription activator for bacteriophage P1 late genes. Mol Microbiol 2003; 48:1621-31. [PMID: 12791143 DOI: 10.1046/j.1365-2958.2003.03533.x] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The stringent starvation protein A (SspA), an Escherichia coli RNA polymerase (RNAP)-associated protein, has been reported to be essential for lytic growth of bacteriophage P1. Unlike P1 early promoters, P1 late promoters are not recognized by RNAP alone. A phage-encoded early protein, Lpa (late promoter activator protein, formerly called gp10), has been shown to be required for P1 late transcription in vivo. Here, we demonstrate that SspA is a transcription activator for P1 late genes. Our results indicated that Lpa is not limiting in an sspA mutant. However, the transcription of P1 late genes was deficient in an sspA mutant in vivo. We demonstrated that SspA/Lpa are required for transcription activation of the P1 late promoter Ps in vitro. In addition, SspA and Lpa were shown to facilitate the binding of RNAP to Ps late promoter DNA. Activation of late transcription by SspA/Lpa was dependent on holoenzyme containing sigma70 but not sigmaS, indicating that the two activators discriminate between the two forms of the holoenzyme. Furthermore, P1 early gene expression was downregulated in the wild-type background, whereas it persisted in the sspA mutant background, indicating that SspA/Lpa mediate the transcriptional switch from the early to the late genes during P1 lytic growth. Thus, this work provides the first evidence for a function of the E. coli RNAP-associated protein SspA.
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Affiliation(s)
- Anne-Marie Hansen
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, 37 Convent Drive, 9000 Rockville Pike, Bethesda, MD 20892-4264, USA
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6
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Schofield DA, Westwater C, Dolan JW, Schmidt MG, Norris JS. Controlled expression in Klebsiella pneumoniae and Shigella flexneri using a bacteriophage P1-derived C1-regulated promoter system. J Bacteriol 2001; 183:6947-50. [PMID: 11698385 PMCID: PMC95537 DOI: 10.1128/jb.183.23.6947-6950.2001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The utility of promoters regulated by the bacteriophage P1 temperature-sensitive C1 repressor was examined in Shigella flexneri and Klebsiella pneumoniae. Promoters carrying C1 operator sites driving LacZ expression had induction/repression ratios of up to 240-fold in S. flexneri and up to 50-fold in K. pneumoniae. The promoters exhibited remarkably low basal expression, demonstrated modulation by temperature, and showed rapid induction. This system will provide a new opportunity for controlled gene expression in enteric gram-negative bacteria.
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Affiliation(s)
- D A Schofield
- Department of Microbiology and Immunology, Medical University of South Carolina, 173 Ashley Ave., Charleston, SC 29403, USA.
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Lehnherr H, Jensen CD, Stenholm AR, Dueholm A. Dual regulatory control of a particle maturation function of bacteriophage P1. J Bacteriol 2001; 183:4105-9. [PMID: 11418548 PMCID: PMC95297 DOI: 10.1128/jb.183.14.4105-4109.2001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2001] [Accepted: 04/19/2001] [Indexed: 11/20/2022] Open
Abstract
A unique arrangement of promoter elements was found upstream of the bacteriophage P1 particle maturation gene (mat). A P1-specific late-promoter sequence with conserved elements located at positions -22 and -10 was expected from the function of the gene in phage morphogenesis. In addition to a late-promoter sequence, a -35 element and an operator sequence for the major repressor protein, C1, were found. The -35 and -10 elements constituted an active Escherichia coli sigma(70) consensus promoter, which was converted into a P1-regulated early promoter by the superimposition of a C1 operator. This combination of early- and late-promoter elements regulates and fine-tunes the expression of the particle maturation gene. During lysogenic growth the gene is turned off by P1 immunity functions. Upon induction of lytic growth, the expression of mat starts simultaneously with the expression of other C1-regulated P1 early functions. However, while most of the latter functions are downregulated during late stages of lytic growth the expression of mat continues throughout the entire lytic growth cycle of bacteriophage P1. Thus, the maturation function has a head start on the structural components of the phage particle.
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Affiliation(s)
- H Lehnherr
- Department of Genetics and Biochemistry, Institute of Microbiology, Ernst-Moritz-Arndt-University Greifswald, D-17487 Greifswald, Germany.
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8
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Abstract
The P1 plasmid addiction operon encodes Doc, a toxin that kills plasmid-free segregants, and Phd, an unstable antidote that neutralizes the toxin. Additionally, these products repress transcription of the operon. The antidote binds to two adjacent sites in the promoter. Here we present evidence concerning the regulatory role of the toxin, which we studied with the aid of a mutation, docH66Y. The DocH66Y protein retained the regulatory properties of the wild-type protein, but not its toxicity. In vivo, DocH66Y enhanced repression by Phd but failed to affect repression in the absence of Phd, suggesting that DocH66Y contacts Phd. In vitro, a MalE-DocH66Y fusion protein was found to bind Phd. Binding of toxin to antidote may be the physical basis for the neutralization of toxin. DocH66Y failed to bind DNA in vitro yet enhanced the affinity, cooperativity, and specificity with which Phd bound the operator. Although DocH66Y enhanced the binding of Phd to two adjacent Phd-binding sites, DocH66Y had relatively little effect on the binding of Phd to a single Phd-binding site, indicating that DocH66Y mediates cooperative interactions between adjacent Phd-binding sites. Several electrophoretically distinct protein-DNA complexes were observed with different amounts of DocH66Y relative to Phd. Maximal repression and specificity of DNA binding were observed with subsaturating amounts of DocH66Y relative to Phd. Analogous antidote-toxin pairs appear to have similar autoregulatory circuits. Autoregulation, by dampening fluctuations in the levels of toxin and antidote, may prevent the inappropriate activation of the toxin.
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Affiliation(s)
- R Magnuson
- Laboratory of Biochemistry, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892-4225, USA.
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9
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Abstract
Amber and deletion mutants were used to assign functions in cell lysis to three late genes of bacteriophage P1. Two of these genes, lydA and lydB of the dar operon, are 330 and 444 bp in length, respectively, with the stop codon of lydA overlapping the start codon of lydB. The third, gene 17, is 558 bp in length and is located in an otherwise uncharacterized operon. A search with the predicted amino acid sequence of LydA for secondary motifs revealed a holin protein-like structure. Comparison of the deduced amino acid sequence of gene 17 with sequences of proteins in the SwissProt database revealed homologies with the proteins of the T4 lysozyme family. The sequence of lydB is novel and exhibited no known extended homology. To study the effect of gp17, LydA, and LydB in vivo, their genes were cloned in a single operon under the control of the inducible T7 promoter, resulting in plasmid pAW1440. A second plasmid, pAW1442, is identical to pAW1440 but has lydB deleted. Induction of the T7 promoter resulted in a rapid lysis of cells harboring pAW1442. In contrast, cells harboring pAW1440 revealed only a small decrease in optical density at 600 nm compared with cells harboring vector alone. The rapid lysis phenotype in the absence of active LydB suggests that this novel protein might be an antagonist of the holin LydA.
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Affiliation(s)
- C Schmidt
- Abteilung Mikrobiologie, Biozentrum Universität Basel, Switzerland
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10
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Abstract
Prophages P1 and P7 exist as unit copy DNA plasmids in the bacterial cell. Maintenance of the prophage state requires the continuous expression of two repressors: (i) C1 is a protein which negatively regulates the expression of lytic genes including the C1 inactivator gene coi, and (ii) C4 is an antisense RNA which specifically inhibits the synthesis of an anti-repressor Ant. In addition, C1 repression is strengthened by lxc encoding an auxiliary repressor protein. The repressors C1, C4 and Lxc are components of a tripartite immunity system of the two phages. Here, the mode of action of these regulatory components including their antagonists Coi and Ant is described.
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Affiliation(s)
- J Heinrich
- Max-Planck-Institut für Molekulare Genetik, Berlin, Germany
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Yang W, Ni L, Somerville RL. A stationary-phase protein of Escherichia coli that affects the mode of association between the trp repressor protein and operator-bearing DNA. Proc Natl Acad Sci U S A 1993; 90:5796-800. [PMID: 8516330 PMCID: PMC46809 DOI: 10.1073/pnas.90.12.5796] [Citation(s) in RCA: 65] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Highly purified preparations of trp repressor (TrpR) protein derived from Escherichia coli strains that were engineered to overexpress this material were found to contain another protein, of 21 kDa. The second protein, designated WrbA [for tryptophan (W) repressor-binding protein] remained associated with its namesake through several sequential protein fractionation steps. The N-terminal amino acid sequence of the WrbA protein guided the design of two degenerate oligonucleotides that were used as probes in the cloning of the wrbA gene (198 codons). The WrbA protein, in purified form, was found by several criteria to enhance the formation and/or stability of noncovalent complexes between TrpR holorepressor and its primary operator targets. The formation of an operator-holorepressor-WrbA ternary complex was demonstrated by gel mobility-shift analysis. The WrbA protein alone does not interact with the trp operator. During the stationary phase, cells deficient in the WrbA protein were less efficient than wild type in their ability to repress the trp promoter. It is proposed that the WrbA protein functions as an accessory element in blocking TrpR-specific transcriptional processes that might be physiologically disadvantageous in the stationary phase of the bacterial life cycle.
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Affiliation(s)
- W Yang
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907-1153
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